chr6-41322112-T-G

Variant names:

• chr6-41322112-T-G
• rs7772334

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.613 in 151,956 control chromosomes in the GnomAD database, including 29,039 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (29039 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93000 AN: 151838 Hom.: 29012 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.611

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.613 AC: 93081 AN: 151956 Hom.: 29039 Cov.: 32 AF XY: 0.613 AC XY: 45547 AN XY: 74258

African (AFR) AF: 0.734 AC: 30412 AN: 41436

American (AMR) AF: 0.674 AC: 10287 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1910 AN: 3464

East Asian (EAS) AF: 0.522 AC: 2685 AN: 5148

South Asian (SAS) AF: 0.503 AC: 2426 AN: 4824

European-Finnish (FIN) AF: 0.557 AC: 5872 AN: 10534

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.553 AC: 37576 AN: 67964

Other (OTH) AF: 0.615 AC: 1298 AN: 2112

Alfa AF: 0.565 Hom.: 12085

Bravo AF: 0.627

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.62
PhyloP100		-0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7772334; hg19: chr6-41289850;